Genescape

The genescape suite is a collection of tools used to visualize the results of functional genome analysis. Various new tools may be implemented in the future.

• tree draws informative Gene Ontology (GO) subgraphs
• annotate annotates a list of genes with GO functions
• web provides a web interface for the tree command

We provide standalone executables for GeneScape that can be run without any installation. The software can also operate in command line mode.

Quick start

Doubleclick the executable to start the program. You will get an interface that looks like this:

Fill in the text box with a list of genes names or GO terms or gene names and click the Draw Tree button to visualize the relationships between the GO terms.

The program will generate a tree visualization.

Note all the options available in the interface:

Color scheme

The colors in the tree carry additional meaning:

• Light Green nodes represent functions that are in the input list.
• Dark green nodes are functions present in the input and are leaf nodes in the terminology, the most granular annotation possible

Each subtree in a different GO category has a different color:

• Biological Process (BP)
• Molecular Function (MF)
• Cellular Component (CC)

The subtree coloring is meant to help you understand the level of detail and the specificity of the functional terms you visualize.

Numbers such as 1/4 mean how many genes in the input carry that function.

Command line usage

See the installation below on how to get the command line version.

To start the web interface type:

genescape web

A web browser will start with the interface above.

genescape tree

You can also use GeneScape completely from the command line with no web interface.

We packaged test data with the software so you can test it like so:

genescape tree --test

Which will generate a tree visualization of the test data.

You can pass to the tree visualizer a list of genes or a list of GO ids, or even a mix of both. Here is an example.

Cyp1a1
Sphk2
Sptlc2

run the tree command to visualize the relationships between the GO terms

genescape tree genes.txt -o output.pdf

You only had three genes in the input yet even that produces a large tree of terms.

You can narrow down the visualization in multiple ways, for example, you can select only terms that match the word lipid :

genescape tree -m lipid genes.txt -o output.pdf

When filtered as shown above the output is much more manageable:

genetrack annotation

The annotator operates on gene names. Suppose you have a list of gene names in the format:

Cyp1a1
Sphk2
Sptlc2
Smpd3

The command:

genescape annotate -t --csv

will produce the output:

gid,root,count,function,source,size,label
GO:0090630,BP,1,activation of GTPase activity,GRTP1,4,(1/4)
GO:0046982,MF,1,protein heterodimerization activity,ABTB3,4,(1/4)
GO:0031083,CC,1,BLOC-1 complex,BCAS4,4,(1/4)
GO:0016020,CC,1,membrane,ABTB3,4,(1/4)
GO:0005737,CC,1,cytoplasm,BCAS4,4,(1/4)
GO:0005615,CC,1,extracellular space,C3P1,4,(1/4)
GO:0005096,MF,1,GTPase activator activity,GRTP1,4,(1/4)
GO:0004866,MF,1,endopeptidase inhibitor activity,C3P1,4,(1/4)

Installation

For a standalone executable, download the latest release from the releases page. We offer executables for Windows and MacOS.

When installed from the command line, the software requires Python 3.10 or above.

You can install genescape via pip or pipx.

pip install genescape

Since the software is meant to be used as a command line tool, pipx is perhaps an even better choice:

pipx install genescape

If you only use the web interface via genescape web no other software installation is needed.

If you want to generate images from the command line without a web browser, you will also need to have the dot software from Graphviz installed and available on your PATH.

You can install Graphviz via your package manager or via conda with:

conda install graphviz

If you are unable to install the dot package you can save the output as .dot files

genescape tree -o graph.dot --demo

Then use an online tool like viz-js to visualize the graph.

License

genescape is distributed under the terms of the MIT license.